The site, insights.london.nhs.uk, was given a black background, eerie music and a message in white text that read: “Hacked by AnoaGhost.”
Cyber-security expert Kevin Beaumont spotted the defacement and tweeted a screenshot of it to his followers on Tuesday afternoon.
A few hours later, the message was removed.
The site in question hosts data from sources such as patient surveys about primary care providers, including GP surgeries.
A cached screenshot of the web page available online suggests it had been compromised for at least five days, though the NHS has not confirmed this was the case.
The removal occurred after NHS Digital, which advises on technical issues for NHS organisations, was contacted by the BBC.
A spokesman for NHS Digital said: “We are aware of this and action has been taken by the site owners to remove the defaced parts of the website.
“We will work with the site owner to help them remediate the underlying vulnerability.”
The BBC has asked NHS England, which owns the affected site, for comment.